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Numbering & Regions

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Region Sequence Details
Regions Definition:
Region Sequence Fragment Residues Length
LFR1
DIQMTQSPSTLSASVGDRVTITC
1 - 23 23
CDR-L1
RASQSISRWLA
24 - 34 11
LFR2
WYQQKPGKVPKLLIY
35 - 49 15
CDR-L2
KASSLES
50 - 56 7
LFR3
GVPSRFSGSGSGTEFTLTISSLQPDDFATYYC
57 - 88 32
CDR-L3
QQYNSYS
89 - 95 7
LFR4
FGPGTKVDIKRTV
96 - 108 13
Tail
AAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKD
STYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC
109 - 212 104
212
Region Sequence Fragment Residues Length
LFR1
DIQMTQSPSTLSASVGDRVTITC
1 - 23 23
CDR-L1
RASQSISRWLA
24 - 34 11
LFR2
WYQQKPGKVPKLLIY
35 - 49 15
CDR-L2
KASSLES
50 - 56 7
LFR3
GVPSRFSGSGSGTEFTLTISSLQPDDFATYYC
57 - 88 32
CDR-L3
QQYNSYS
89 - 95 7
LFR4
FGPGTKVDIKRTV
96 - 108 13
Tail
AAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKD
STYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC
109 - 212 104
212
Region Sequence Fragment Residues Length
LFR1
DIQMTQSPSTLSASVGDRVTITC
1 - 23 23
CDR-L1
RASQSISRWLA
24 - 34 11
LFR2
WYQQKPGKVPKLLIY
35 - 49 15
CDR-L2
KASSLES
50 - 56 7
LFR3
GVPSRFSGSGSGTEFTLTISSLQPDDFATYYC
57 - 88 32
CDR-L3
QQYNSYS
89 - 95 7
LFR4
FGPGTKVDIKRTV
96 - 108 13
Tail
AAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKD
STYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC
109 - 212 104
212
Region Sequence Fragment Residues Length
LFR1
DIQMTQSPSTLSASVGDRVTITCRASQSI
1 - 29 29
CDR-L1
SRWLAWY
30 - 36 7
LFR2
QQKPGKVPK
37 - 45 9
CDR-L2
LLIYKASSLE
46 - 55 10
LFR3
SGVPSRFSGSGSGTEFTLTISSLQPDDFATYYC
56 - 88 33
CDR-L3
QQYNSY
89 - 94 6
LFR4
SFGPGTKVDIKRTV
95 - 108 14
Tail
AAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKD
STYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC
109 - 212 104
212
Region Sequence Fragment Residues Length
LFR1
DIQMTQSPSTLSASVGDRVTITCRAS
1 - 26 26
CDR-L1
QSISRW
27 - 32 6
LFR2
LAWYQQKPGKVPKLLIY
33 - 49 17
CDR-L2
KA
50 - 51 2
LFR3
SSLESGVPSRFSGSGSGTEFTLTISSLQPDDFATYYC
52 - 88 37
CDR-L3
QQYNSYS
89 - 95 7
LFR4
FGPGTKVDIKRTV
96 - 108 13
Tail
AAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKD
STYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC
109 - 212 104
212
Region Definition Sequence Fragment Residues Length
LFR1 Chothia
DIQMTQSPSTLSASVGDRVTITC------
1 - 23 23
AbM
DIQMTQSPSTLSASVGDRVTITC------
1 - 23 23
Kabat
DIQMTQSPSTLSASVGDRVTITC------
1 - 23 23
Contact
DIQMTQSPSTLSASVGDRVTITCRASQSI
1 - 29 29
IMGT
DIQMTQSPSTLSASVGDRVTITCRAS---
1 - 26 26
CDR-L1 Chothia
RASQSISRWLA--
24 - 34 11
AbM
RASQSISRWLA--
24 - 34 11
Kabat
RASQSISRWLA--
24 - 34 11
Contact
------SRWLAWY
30 - 36 7
IMGT
---QSISRW----
27 - 32 6
LFR2 Chothia
--WYQQKPGKVPKLLIY
35 - 49 15
AbM
--WYQQKPGKVPKLLIY
35 - 49 15
Kabat
--WYQQKPGKVPKLLIY
35 - 49 15
Contact
----QQKPGKVPK----
37 - 45 9
IMGT
LAWYQQKPGKVPKLLIY
33 - 49 17
CDR-L2 Chothia
----KASSLES
50 - 56 7
AbM
----KASSLES
50 - 56 7
Kabat
----KASSLES
50 - 56 7
Contact
LLIYKASSLE-
46 - 55 10
IMGT
----KA-----
50 - 51 2
LFR3 Chothia
-----GVPSRFSGSGSGTEFTLTISSLQPDDFATYYC
57 - 88 32
AbM
-----GVPSRFSGSGSGTEFTLTISSLQPDDFATYYC
57 - 88 32
Kabat
-----GVPSRFSGSGSGTEFTLTISSLQPDDFATYYC
57 - 88 32
Contact
----SGVPSRFSGSGSGTEFTLTISSLQPDDFATYYC
56 - 88 33
IMGT
SSLESGVPSRFSGSGSGTEFTLTISSLQPDDFATYYC
52 - 88 37
CDR-L3 Chothia
QQYNSYS
89 - 95 7
AbM
QQYNSYS
89 - 95 7
Kabat
QQYNSYS
89 - 95 7
Contact
QQYNSY-
89 - 94 6
IMGT
QQYNSYS
89 - 95 7
LFR4 Chothia
-FGPGTKVDIKRTV
96 - 108 13
AbM
-FGPGTKVDIKRTV
96 - 108 13
Kabat
-FGPGTKVDIKRTV
96 - 108 13
Contact
SFGPGTKVDIKRTV
95 - 108 14
IMGT
-FGPGTKVDIKRTV
96 - 108 13
Humanness

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Accession & Annotations
Accession 1dfb_L
Source PDB  1dfb  Submitted 27-MAR-1992  Updated 25-AUG-2009
Name
STRUCTURE OF A HUMAN MONOCLONAL ANTIBODY FAB FRAGMENT AGAINST GP41 OF HUMAN IMMUNODEFICIENCY VIRUS TYPE I
Organism
Homo sapiens
Human Subgroup Kappa Light chain subgroup I
Chain Type Light
Pairing 1dfb_H
Identical Protein Sequences PDB: 7n07_L 7n08_B 7n08_D 7n08_L
References
HE M., RUKER F., CASALE E., CARTER C.
'STRUCTURE OF A HUMAN MONOCLONAL ANTIBODY FAB FRAGMENT AGAINST GP41 OF HUMAN IMMUNODEFICIENCY VIRUS TYPE 1.'
PROC.NATL.ACAD.SCI.USA V. 89 7154 1992 ISSN 0027-8424
Sequences
Amino Acid Sequence:
DIQMTQSPSTLSASVGDRVTITCRASQSISRWLAWYQQKPGKVPKLLIYKASSLESGVPS
RFSGSGSGTEFTLTISSLQPDDFATYYCQQYNSYSFGPGTKVDIKRTVAAPSVFIFPPSD
EQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLS
KADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

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Germline Tools
Data Source:
Data Source V D J Exclude if warnings
NCBI Germline
V-BASE
Alignment settings:
Rank alignments by
Exclude identical hits
Search settings:
V-segment score threshold
D-segment score threshold
J-segment score threshold
Gaps:
Gap penalty

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abYmod homology modelling

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Energy minimised    
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Chains
1dfb_H
All Heavy
All HFR
All CDR-H
HFR1
CDR-H1
HFR2
CDR-H2
HFR3
CDR-H3
HFR4
Other Heavy
1dfb_L
All Light
All LFR
All CDR-L
LFR1
CDR-L1
LFR2
CDR-L2
LFR3
CDR-L3
LFR4
Other Light
Colours
Labels
On
Off
Atoms
Main chain
All
Style
Wireframe
Ball and Stick
Spacefill
Cartoon
Backbone
Reset
Black
Reset
White

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